Variant report

Variant	rs17109371
Chromosome Location	chr14:25429892-25429893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10132357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10132944	0.87[CEU][hapmap]
rs10134048	0.87[CEU][hapmap];0.91[TSI][hapmap]
rs10138510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151968	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs11628502	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11847576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11849185	0.94[ASN][1000 genomes]
rs11850786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11850957	0.87[GIH][hapmap]
rs11851504	0.94[ASN][1000 genomes]
rs17109366	0.87[CEU][hapmap];0.87[TSI][hapmap]
rs17109380	0.98[ASN][1000 genomes]
rs17109382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17109397	0.94[ASN][1000 genomes]
rs17109406	0.87[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs17109457	0.91[ASN][1000 genomes]
rs17109462	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.94[ASN][1000 genomes]
rs1952491	0.91[ASN][1000 genomes]
rs1952499	0.91[ASN][1000 genomes]
rs2093714	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs2094659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28625718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28722832	0.96[ASN][1000 genomes]
rs35106416	0.91[ASN][1000 genomes]
rs57426267	0.91[ASN][1000 genomes]
rs57614343	0.91[ASN][1000 genomes]
rs58424382	0.98[ASN][1000 genomes]
rs58590969	0.91[ASN][1000 genomes]
rs7142073	0.94[ASN][1000 genomes]
rs7147314	0.93[EUR][1000 genomes]
rs7152812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7153837	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7154613	0.91[ASN][1000 genomes]
rs7155485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7155878	1.00[CEU][hapmap]
rs7158164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724116	0.87[CEU][hapmap];0.91[TSI][hapmap]
rs8004566	0.91[ASN][1000 genomes]
rs8008618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8009099	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8017710	0.87[CEU][hapmap]
rs8019222	0.94[ASN][1000 genomes]
rs8021478	0.87[CEU][hapmap];0.91[TSI][hapmap]
rs987056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901508	chr14:25365505-25451903	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1041051	chr14:25388230-25480511	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1047792	chr14:25388933-25503799	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17109371	LTB4R2	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25422600-25434000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr14:25424600-25460600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr14:25426200-25430000	Enhancers	Brain Anterior Caudate	brain
4	chr14:25426400-25435000	Weak transcription	Aorta	Aorta
5	chr14:25426600-25430600	Enhancers	Fetal Intestine Small	intestine
6	chr14:25426800-25430600	Enhancers	Colon Smooth Muscle	Colon
7	chr14:25427000-25430000	Enhancers	Rectal Smooth Muscle	rectum
8	chr14:25427000-25430400	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr14:25427000-25430600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr14:25427200-25430600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr14:25427200-25430600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr14:25427400-25430200	Enhancers	Brain Cingulate Gyrus	brain
13	chr14:25427400-25430600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:25427400-25430600	Enhancers	Fetal Intestine Large	intestine
15	chr14:25427400-25431000	Enhancers	Stomach Smooth Muscle	stomach
16	chr14:25427600-25430200	Enhancers	Brain Substantia Nigra	brain
17	chr14:25427800-25430400	Enhancers	Fetal Heart	heart
18	chr14:25427800-25430600	Enhancers	Fetal Stomach	stomach
19	chr14:25428000-25430000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr14:25428000-25430000	Enhancers	NHLF	lung
21	chr14:25428000-25430200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr14:25428000-25430400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr14:25428000-25430600	Enhancers	Brain Angular Gyrus	brain
24	chr14:25428200-25430000	Enhancers	Duodenum Mucosa	Duodenum
25	chr14:25428200-25435000	Weak transcription	Osteobl	bone
26	chr14:25428400-25430000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr14:25428400-25430000	Enhancers	Fetal Muscle Leg	muscle
28	chr14:25428400-25430000	Enhancers	Lung	lung
29	chr14:25428400-25430000	Enhancers	Psoas Muscle	Psoas
30	chr14:25428400-25430000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr14:25428400-25430000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr14:25428400-25430000	Enhancers	GM12878-XiMat	blood
33	chr14:25428400-25430200	Enhancers	Small Intestine	intestine
34	chr14:25428400-25430600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:25428400-25430600	Enhancers	Brain Hippocampus Middle	brain
36	chr14:25428600-25430400	Enhancers	HepG2	liver
37	chr14:25428800-25430000	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr14:25428800-25434800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr14:25429000-25430000	Enhancers	Liver	Liver
40	chr14:25429000-25430000	Enhancers	Left Ventricle	heart
41	chr14:25429000-25430000	Enhancers	Pancreas	Pancrea
42	chr14:25429000-25430000	Enhancers	Right Ventricle	heart
43	chr14:25429200-25430000	Enhancers	Colonic Mucosa	Colon
44	chr14:25429200-25430000	Enhancers	Gastric	stomach
45	chr14:25429200-25430400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr14:25429400-25433400	Weak transcription	Stomach Mucosa	stomach
47	chr14:25429400-25434200	Weak transcription	HSMM	muscle
48	chr14:25429600-25430000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr14:25429600-25430000	Weak transcription	Fetal Lung	lung
50	chr14:25429600-25433400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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